callPrimer3 {SPLINTER} | R Documentation

## callPrimer3

### Description

call primer3 for a given set of DNAstringSet object

### Usage

    callPrimer3(seq, size_range = "150-500", Tm = c(57, 59, 62),
      name = "Primer1", primer3 = "primer3-2.3.7/bin/primer3_core",
      thermo.param = "primer3-2.3.7/src/primer3_config/",
      sequence_target = NULL,
      settings = "primer3-2.3.7/primer3web_v4_0_0_default_settings.txt")

### Arguments

`seq` | DNAstring object, one DNA string for the given amplicon
`size_range` | default: '151-500'
`Tm` | melting temprature parameters default:c(55,57,58)
`name` | name of the amplicon in chr_start_end format
`primer3` | primer3 path
`thermo.param` | thermodynamic parameters folder
`sequence_target` | If one or more targets is specified then a legal primer pair must flank at least one of them.
`settings` | text file for parameters

### Details

modified to include SEQUENCE_TARGET as an option

### Value

data.frame of designed primers and parameters

### Author(s)

Altuna Akalin's modified Arnaud Krebs' original function further modified here by Diana Low

### Examples

    ### NOT RUN ###
    # primer_results<-callPrimer3(seq='')

[Package SPLINTER version 1.8.1 Index]